Main
Rui Fu
RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus
My research interests are in various aspects of post-transcriptional gene expression regulation, particularly RNA degradation, interrogated through both biochemical experiments and bioinformatic/computational analyses of genomic and sequencing data.
Education
Ph.D. Biological Science
University of California San Diego
La Jolla, CA, USA
2015 - 2009
B.S. Biological Science
Xiamen University
Xiamen, Fujian, China
2009 - 2005
Research Experience
Bioinformatic tool development:
clustifyr, automated single cell RNA-seq cell identity assignment Bioconductor package (author)
squirrelBox, RNA-seq data visualization, exploration, and analysis web browser built with R Shiny and JavaScript (author)
someta, quantification and monitoring of missing cell-level metadata in scRNA-seq GEO deposition (author)
valr, framework for tidyverse-style genomic interval analysis in R (co-developer)
scraps, scalable pipeline for extraction of polyadenylation site information from scRNA-seq data (co-developer)
Semi-Independent Postdoctoral Informatics Fellow
Jay Hesselberth’s Supervision
University of Colorado Anschutz
Current - 2017
- Development of bioinformatics software packages
- RNA post-transcriptional dynamics modeling of steroidogenesis
- RNA-seq analysis and transcriptome annotation improvements for hibernating ground squirrel brain
- Collaboration on various RNA biology projects
Postdoctoral Research Fellow
Judy Lieberman’s Lab
Harvard Medical School
2017 - 2016
- Identification of a mitochondrial trigger for apoptotic mRNA decay
- Purification of cytotoxic granules and cytolytic proteins from NK cells
- Mouse genetic manipulation by CRISPR-Cas9, and automated genotyping with custom R app
Graduate Research Assistant
Jens Lykke-Andersen’s Lab
University of California San Diego
2015 - 2009
- Investigation of co-factors involved in ZFP36-mediated mRNA decay and translational repression during macrophage innate immune response
- Characterization of the ZFP36 family proteins in cell cycle progression regulation of mouse embryonic fibroblasts
Undergraduate Research Assistant
Ruichuan Chen’s Lab
Xiamen University
2009 - 2007
- Exploration of cell cycle and apoptosis implications of the transcription elongation regulator HEXIM1
- Mechanistic characterization of p-TEFb activation by HIV-Tat
Teaching Experience
Additional pedagogy training through the Harvard Medical School Scientists Teaching Science Course
Developed computational biology course materials:
rnabioco.github.io/practical-data-analysis
rnabioco.github.io/cellar
Online Lecture Instructor (Graduate Level Courses)
University of Colorado Anschutz
N/A
- Informatics and Statistics for Molecular Biology (2020) - teaching and grading on RStudio Cloud platform
- Foundations in Biomedical Sciences (2020) - online lecture, paper discussion, and homework/exam design on RNA biology
- Workshop for scRNA-seq Data Analysis (2020) - course development and online lectures
Lecture Instructor (Graduate Level Courses)
University of Colorado Anschutz
N/A
- Rigor in Research (2020) - lecture on RNA sequencing
- Foundations in Biomedical Sciences (2018, 2019) - lectures, paper discussion, and homework/exam design on RNA biology
- Practical Data Analysis with R/RStudio (2018, 2019) - course development and lectures
- Workshop for scRNA-seq Data Analysis (2019) - course development and lectures
Teaching Assistant (Graduate Level Courses)
University of Colorado Anschutz
N/A
- Practical Computational Biology for Biologists: R (2018, 2019)
- Practical Computational Biology for Biologists: Python (2018, 2019)
- Paper discussion for Core Topics in Biomedical Sciences (2018)
Weekly RNA Bioscience Initiative Informatics Office Hour
University of Colorado Anschutz
N/A
- Guidance on RNA and computational research questions from students and researchers of CU Anschutz Medical Campus
Teaching Assistant (Undergraduate Level Courses)
University of California San Diego
N/A
- Molecular Biology (2012)
- DNA Recombination Lab (2011, 2012)
Mentoring Experience
RNA Bioscience Initiative Internship Mentoring
University of Colorado Anschutz
N/A
Current - 2020
- Mentoring of undergraduate computer science student, systemically exploring published scRNA-seq cell type signatures in the NCBI Gene Expression Omnibus
- Mentee’s work was integrated into recent updates to R Bioconductor packages clustifyr and clustifyrdatahub
- Mentoring is continuing beyond summer intern period, now focusing on manuscript preparation, poster presentation, and further scRNA-seq software development
Summer Research Mentoring
Harvard Medical School
N/A
2017
- Mentoring of high school student enrolled in the MIT Research Science Institute program on tissue culture, RNA-related bench experiments, RNA-seq informatics analysis, and scientific writing
BS/MS Student Research Mentoring
University of California San Diego
N/A
2015 - 2013
- Mentoring of student research spanning undergraduate honor thesis and master thesis on biochemical investigations of RNA-binding protein functions
- Mentee was awarded Best Poster Presentation Award at 2014 UCSD Biological Sciences Annual Student Research Showcase
- Research project was integrated into 2016 RNA publication, with mentee as second author
Posters and Talks
clustifyr2.0: leveraging GEO deposited single cell data for automated cell type classification
Keystone eSymposia on Single Cell Biology (Poster)
N/A
2021
Towards a comprehensive view of dynamic RNA regulation in hibernating 13-lined ground squirrel
EMBL Conference, From Functional Genomics to Systems Biology (Poster)
N/A
2020
ClustifyR: automated single-cell RNA sequencing cluster classification
Keystone Symposia on Single Cell Biology (Poster)
N/A
2019
PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA and poly(A)-tailed ncRNA during apoptosis
Boston Children’s Hospital PCMM Research Poster Session (Poster)
N/A
2017
PNPT1 release from the mitochondrial intermembrane space triggers rapid decay of mRNA during apoptosis
Boston Children’s Hospital PCMM Research Poster Session (Poster)
N/A
2016
TTP-mediated mRNA repression involves recruitment of the 4EHP-GYF2 complex
Cold Spring Harbor Laboratory mRNA Processing Meeting (Presentation)
N/A
2015
TTP represses translation of target mRNAs through the 4EHP-GYF2 complex
UCSD Mechanisms of Gene Expression Seminar (Presentation)
N/A
2014
TTP family proteins regulate the stability of retinoblastoma protein mRNAs during serum-stimulated G0-S transition
Cold Spring Harbor Laboratory mRNA Processing Meeting (Poster)
N/A
2013
The regulation of TTP family mRNA-decay factors during G0-S cell cycle progression
Keystone Symposia on Protein-RNA Interactions (Poster)
N/A
2012
Professional Service
Society memberships:
RNA Society
International Society for Computational Biology
Genetics Society of America
Organizer for CU Anschutz Immuno-Informatics Joint Journal Club
N/A
N/A
Current - 2020
RNA Bioscience Initiative Grant Review
N/A
N/A
Current - 2019
GENETICS Early Career Reviewer (Cellular Genetics section)
4 manuscripts reviewed for GENETICS and G3, tinyurl.com/rev-rf
N/A
Current - 2018
Peer review of manuscripts under Dr Lykke-Andersen, Dr Lieberman, Dr Hesselberth
N/A
N/A
Current - 2011
Organizer for UCSD Ethics Center’s Silent Spring (50th Anniversary) Project
N/A
N/A
2012
Diversity, Equity, and Inclusion Service
RNA Society Volunteer - Writer for Scientist Spotlight
N/A
N/A
Current - 2020
CU Anschutz Medical Campus Equity Certificate Program training
N/A
N/A
2021
Admissions Committee for CU Graduate Experiences for Multicultural Students
N/A
N/A
2019
Mentor for CU Anschutz and Denver Campus ISCORE (undergraduate mentorship program)
N/A
N/A
2019
Recognition and Training
BioFrontiers Hackathon
N/A
N/A
2018
Data Incubator Data Science Fellowship
N/A
N/A
2017
Grant writing training under Dr Lieberman
N/A
N/A
2016
Harvard Medical School Scientists Teaching Science Course
N/A
N/A
2016
Dr Huang Memorial Scholarship, UC San Diego
N/A
N/A
2011 - 2009
National College Students Creativity Experiment Project
N/A
N/A
2009 - 2007
First-Class Scholarship
N/A
N/A
2008 - 2006
XMU University Merit Student
N/A
N/A
2008 - 2006
Science Outreach
~500 hours of weekend volunteering time logged
Volunteer for CU Anschutz Medical Campus Young Hands in Science Outreach Program
N/A
N/A
2021
Facilitator at Denver Museum of Nature and Science - Prehistoric Journey section
N/A
N/A
2020 - 2019
Visitor Education Volunteer at the New England Aquarium
N/A
N/A
2017 - 2016
Information Ambassador at the San Diego Zoo
N/A
N/A
2016 - 2015